Misidentified biomedical resources: Journal guidelines are not a quick fix.
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ABSTRACT:
SUBMITTER: Hepkema WM
PROVIDER: S-EPMC9300184 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The inexorable demographic momentum of the global human population is rapidly eroding Earth's life-support system. There are consequently more frequent calls to address environmental problems by advocating further reductions in human fertility. To examine how quickly this could lead to a smaller human population, we used scenario-based matrix modeling to project the global population to the year 2100. Assuming a continuation of current trends in mortality reduction, even a rapid transition to a worldwide one-child policy leads to a population similar to today's by 2100. Even a catastrophic mass mortality event of 2 billion deaths over a hypothetical 5-y window in the mid-21(st) century would still yield around 8.5 billion people by 2100. In the absence of catastrophe or large fertility reductions (to fewer than two children per female worldwide), the greatest threats to ecosystems--as measured by regional projections within the 35 global Biodiversity Hotspots--indicate that Africa and South Asia will experience the greatest human pressures on future ecosystems. Humanity's large demographic momentum means that there are no easy policy levers to change the size of the human population substantially over coming decades, short of extreme and rapid reductions in female fertility; it will take centuries, and the long-term target remains unclear. However, some reduction could be achieved by midcentury and lead to hundreds of millions fewer people to feed. More immediate results for sustainability would emerge from policies and technologies that reverse rising consumption of natural resources.
| S-EPMC4246304 | biostudies-literature
Project description:ObjectiveTo investigate the effect of an additional review based on reporting guidelines such as STROBE and CONSORT on quality of manuscripts.DesignMasked randomised trial. Population Original research manuscripts submitted to the Medicina Clínica journal from May 2008 to April 2009 and considered suitable for publication.InterventionControl groupconventional peer reviews alone. Intervention group: conventional review plus an additional review looking for missing items from reporting guidelines. Outcomes Manuscript quality, assessed with a 5 point Likert scale (primary: overall quality; secondary: average quality of specific items in paper). Main analysis compared groups as allocated, after adjustment for baseline factors (analysis of covariance); sensitivity analysis compared groups as reviewed. Adherence to reviewer suggestions assessed with Likert scale.ResultsOf 126 consecutive papers receiving conventional review, 34 were not suitable for publication. The remaining 92 papers were allocated to receive conventional reviews alone (n=41) or additional reviews (n=51). Four papers assigned to the conventional review group deviated from protocol; they received an additional review based on reporting guidelines. We saw an improvement in manuscript quality in favour of the additional review group (comparison as allocated, 0.25, 95% confidence interval -0.05 to 0.54; as reviewed, 0.33, 0.03 to 0.63). More papers with additional reviews than with conventional reviews alone improved from baseline (22 (43%) v eight (20%), difference 23.6% (3.2% to 44.0%), number needed to treat 4.2 (from 2.3 to 31.2), relative risk 2.21 (1.10 to 4.44)). Authors in the additional review group adhered more to suggestions from conventional reviews than to those from additional reviews (average increase 0.43 Likert points (0.19 to 0.67)).ConclusionsAdditional reviews based on reporting guidelines improve manuscript quality, although the observed effect was smaller than hypothesised and not definitively demonstrated. Authors adhere more to suggestions from conventional reviews than to those from additional reviews, showing difficulties in adhering to high methodological standards at the latest research phases. To boost paper quality and impact, authors should be aware of future requirements of reporting guidelines at the very beginning of their study. Trial registration and protocol Although registries do not include trials of peer review, the protocol design was submitted to sponsored research projects (Instituto de Salud Carlos III, PI081903).
| S-EPMC3222149 | biostudies-literature
Project description:Recent advances in molecular biology and computational power have seen the biomedical sector enter a new era, with corresponding development of Bioinformatics as a major discipline. Generation of enormous amounts of data has driven the need for more advanced storage solutions and shared access through a range of public repositories. The number of such biomedical resources is increasing constantly and mining these large and diverse data sets continues to present real challenges. This paper attempts a general overview of currently available resources, together with remarks on their data mining and analysis capabilities. Of interest here is the recent shift in focus from genetic to epigenetic/epigenomic research and the emergence and extension of resource provision to support this both at local and global scale. Biomedical text and numerical data mining are both considered, the first dealing with automated methods for analyzing research content and information extraction, and the second (broadly) with pattern recognition and prediction. Any summary and selection of resources is inherently limited, given the spectrum available, but the aim is to provide a guideline for the assessment and comparison of currently available provision, particularly as this relates to epigenetics/epigenomics.
| S-EPMC3515018 | biostudies-literature
Project description:BackgroundPeer review is widely used in academic fields to assess a manuscript's significance and to improve its quality for publication. This scoping review will assess existing peer review guidelines and/or checklists intended for reviewers of biomedical journals and provide an overview on the review guidelines.MethodsPubMed, Embase, and Allied and Complementary Medicine (AMED) databases were searched for review guidelines from the date of inception until February 19, 2021. There was no date restriction nor article type restriction. In addition to the database search, websites of journal publishers and non-publishers were additionally hand-searched.ResultsOf 14,633 database publication records and 24 website records, 65 publications and 14 websites met inclusion criteria for the review (78 records in total). From the included records, a total of 1,811 checklist items were identified. The items related to Methods, Results, and Discussion were found to be the highly discussed in reviewer guidelines.ConclusionThis review identified existing literature on peer review guidelines and provided an overview of the current state of peer review guides. Review guidelines were varying by journals and publishers. This calls for more research to determine the need to use uniform review standards for transparent and standardized peer review.Protocol registrationThe protocol for this study has been registered at Research Registry (www.researchregistry.com): reviewregistry881.
| S-EPMC8136639 | biostudies-literature
Project description:Most bioinformatics tools available today were not written by professional software developers, but by people that wanted to solve their own problems, using computational solutions and spending the minimum time and effort possible, since these were just the means to an end. Consequently, a vast number of software applications are currently available, hindering the task of identifying the utility and quality of each. At the same time, this situation has hindered regular adoption of these tools in clinical practice. Typically, they are not sufficiently developed to be used by most clinical researchers and practitioners. To address these issues, it is necessary to re-think how biomedical applications are built and adopt new strategies that ensure quality, efficiency, robustness, correctness and reusability of software components. We also need to engage end-users during the development process to ensure that applications fit their needs. In this review, we present a set of guidelines to support biomedical software development, with an explanation of how they can be implemented and what kind of open-source tools can be used for each specific topic.
| S-EPMC5383938 | biostudies-literature
Project description:Cloud computing has revolutionized the development and operations of hardware and software across diverse technological arenas, yet academic biomedical research has lagged behind despite the numerous and weighty advantages that cloud computing offers. Biomedical researchers who embrace cloud computing can reap rewards in cost reduction, decreased development and maintenance workload, increased reproducibility, ease of sharing data and software, enhanced security, horizontal and vertical scalability, high availability, a thriving technology partner ecosystem, and much more. Despite these advantages that cloud-based workflows offer, the majority of scientific software developed in academia does not utilize cloud computing and must be migrated to the cloud by the user. In this article, we present 11 quick tips for architecting biomedical informatics workflows on compute clouds, distilling knowledge gained from experience developing, operating, maintaining, and distributing software and virtualized appliances on the world's largest cloud. Researchers who follow these tips stand to benefit immediately by migrating their workflows to cloud computing and embracing the paradigm of abstraction.
| S-EPMC5875741 | biostudies-literature
Project description:Background:Despite the widespread use of antibodies as a research tool, problems with specificity, lot-to-lot consistency and sensitivity commonly occur and may be important contributing factors to the 'replication crisis' in biomedical research. This makes the validation of antibodies and accurate reporting of this validation in the scientific literature extremely important. Therefore, some journals now require authors to comply with antibody reporting guidelines. Methods:We used a quasi-experimental approach to assess the effectiveness of such journal guidelines in improving antibody reporting in the scientific literature. In a sample of 120 publications, we compared the reporting of antibody validation and identification information in two journals with guidelines (Nature and the Journal of Comparative Neurology) with two journals without guidelines (Science and Neuroscience), before and after the introduction of these guidelines. Results:Our results suggest that the implementation of antibody reporting guidelines might have some influence on the reporting of antibody validation information. The percentage of validated antibodies per article slightly increased from 39% to 57% in journals with guidelines, whereas this percentage decreased from 23% to 14% in journals without guidelines. Furthermore, the reporting of validation information of all primary antibodies increased by 23 percentage points in the journals with guidelines (OR = 2.80, 95% CI = 0.96-INF; adjusted p = 1, one-tailed), compared to a decrease of 13 percentage points in journals without guidelines. Fortunately, the guidelines seem to be more effective in improving the reporting of antibody identification information. The reporting of identification information of all primary antibodies used in a study increased by 58 percentage points (OR = 17.8, 95% CI = 4.8-INF; adjusted p = 0.0003, one-tailed) in journals with guidelines. This percentage also slightly increased in journals without guidelines (by 18 percentage points), suggesting an overall increased awareness of the importance of antibody identifiability. Moreover, this suggests that reporting guidelines mostly have an influence on the reporting of information that is relatively easy to provide. A small increase in the reporting of validation by referencing the scientific literature or the manufacturer's data also indicates this. Conclusion:Combined with the results of previous studies on journal guidelines, our study suggests that the effect of journal antibody guidelines on validation practices by themselves may be limited, since they mostly seem to improve antibody identification instead of actual experimental validation. These guidelines, therefore, may require additional measures to ensure effective implementation. However, due to the explorative nature of our study and our small sample size, we must remain cautious towards other factors that might have played a role in the observed change in antibody reporting behaviour.
| S-EPMC7275675 | biostudies-literature
Project description:ObjectiveThe research analyzes usage of a major biomedical library's pre-1993 print journal collection.MethodologyIn July 2003, in preparation for a renovation and expansion project, the Biomedical Library at the University of California, San Diego, moved all of its pre-1993 journal volumes off-site, with the exception of twenty-two heavily used titles. Patrons wishing to consult one of these stored volumes could request that it be delivered to the library for their use. In the spring of 2006, an analysis was made of these requests.ResultsBy July of 2006, 79,827 journal volumes published in 1992 or earlier had been requested from storage. The number of requests received declined with age of publication. The usage distribution exhibited a "long tail": 50% of the 79,827 requests were for journal volumes published before 1986. The availability of electronic access dramatically reduced the chance that corresponding print journal volumes would be requested.ConclusionsThe older biomedical print journal literature appears to be of continued value to the biomedical research community. When electronic access was provided to the older literature, demand for older print volumes declined dramatically.
| S-EPMC2212321 | biostudies-literature
Project description:ObjectiveTo generate an understanding of the communication practices that might influence the peer-review process in biomedical journals.MethodRecruitment was based on purposive maximum variation sampling. We conducted semistructured interviews. Data were analysed using thematic analysis method.Participants56 journal editors from general medicine (n=13) and specialty (n=43) biomedical journals. Most were editor-in-chiefs (n=39), men (n=40) and worked part time (n=50).ResultsOur analysis generated four themes (1) providing minimal guidance to peer reviewers-two subthemes described the way journal editors rationalised their behaviour: (a) peer reviewers should know without guidelines how to review and (b) detailed guidance and structure might have a negative effect; (2) communication strategies of engagement with peer reviewers-two opposing strategies that journal editors employed to handle peer reviewers: (a) use of direct and personal communication to motivate peer reviewers and (b) use of indirect communication to avoid conflict; (3) concerns about impact of review model on communication-maintenance of anonymity as a means of facilitating critical and unburdened communication and minimising biases and (4) different practices in the moderation of communication between authors and peer reviewers-some journal editors actively interjected themselves into the communication chain to guide authors through peer reviewers' comments, others remained at a distance, leaving it to the authors to work through peer reviewers' comments.ConclusionsThese journal editors' descriptions reveal several communication practices that might have a significant impact on the peer-review process. Editorial strategies to manage miscommunication are discussed. Further research on these proposed strategies and on communication practices from the point of view of authors and peer reviewers is warranted.
| S-EPMC7430556 | biostudies-literature
Project description:Hodgkin lymphoma is a haematological malignancy predominantly affecting young adults. Hodgkin lymphoma is a highly curable disease by current treatment standards. Latest treatment guidelines for Hodgkin lymphoma however imply access to diagnostic and treatment modalities that may not be available in settings with restricted healthcare resources. Considerable discrepancies in Hodgkin lymphoma patient survival exist, with poorer outcomes reported in resources-constrained settings. Resources-stratified guidelines for diagnosis, staging and treatment of Hodgkin lymphoma were derived in an effort to optimize patient outcome provided a given setting of available resources. These guidelines were derived based on the framework of the Breast Health Global Initiative stratifying resource levels in basic, core, advanced and maximal categories.
| S-EPMC7084688 | biostudies-literature